Use of gene expression profiling to predict survival in cancer patient

ABSTRACT

Gene expression profiling in multiple myeloma patients identifies genes that distinguish between patients with subsequent early death or long survival after treatment. Poor survival is linked to over-expression of genes such as ASPM, OPN3 and CKS1B which are located in chromosome 1q. Given the frequent amplification of 1q in many cancers, it is possible that these genes can be used as powerful prognostic markers and therapeutic targets for multiple myeloma and other cancer.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.13/899,196, filed May 21, 2013, now U.S. Pat. No. 9,650,677, which is acontinuation of U.S. application Ser. No. 11/133,937, filed May 20,2005, now U.S. Pat. No. 8,843,320, which claims the benefit of U.S.Provisional Application No. 60/606,319, filed on Sep. 1, 2004, and60/573,669, filed May 21, 2004. The entire teachings of U.S. applicationSer. No. 11/133,937 are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under R33 CA97513-01awarded by the National Institutes of Health. The government has certainrights in the invention.

BACKGROUND OF THE INVENTION

The present invention relates generally to the field of cancer research.More specifically, the present invention relates to gene expressionprofiling in cancer patients.

SUMMARY OF THE INVENTION

Global gene expression profiling has emerged as powerful tool forclassifying disease subtypes and developing robust prognostic models inleukemia and lymphoma (Shipp et al., 2002; Yeoh et al., 2002; Rosenwaldet al., 2002; Bullinger et al., 2004; Valk et al., 2004). Microarraystudies in myeloma have also provided key insights into its biology andclinical behavior (Zhan et al., 2002; De Vos et al., 2002; Claudio etal., 2003; Tian et al., 2003).

In the present invention, gene expression profiles of malignant plasmacells were examined in an effort to identify the molecular signatures ofearly treatment failure after high dose chemotherapy and autologousperipheral blood stem cell transplantation. Results disclosed hereinreveal a clear gene expression signature that portends for a highlyaggressive form of multiple myeloma. Markers identified herein areuseful for initial staging and disease follow-up for prediction ofrelapse of multiple myeloma and other types of cancer. Moreover, thesepredictive genes, their protein products and the biological pathways inwhich they function represent potential points of therapeuticintervention for multiple myeloma and other types of cancer.

The present invention provides a method of determining the prognosis ofa multiple myeloma patient based on reduced expression, overexpressionor their combination of one or more genes discussed herein.

The present invention also provides a method of determining theprognosis of a multiple myeloma patient based in decreased copy number,increased copy number or their combinations of one or more genesdiscussed herein. The present invention further provides a method ofdetermining the risk of developing a disease-related event for a cancerpatient based on overexpression of one or more of the genes identifiedherein as being overexpressed. The present invention still furtherprovides a method of using agents that downregulate the expression ofCKS1B gene or CKS1B gene product to treat a cancer patient havingoverexpression of CKS1B. The present invention also provides a method ofusing compounds that downregulate the expression of CKS1B gene or CKS1Bgene product and a vector comprising DNA sequence encoding RFP2 gene totreat an individual having high-risk multiple myeloma.

The present invention further provides a kit comprising (a) probespecific for CKS1B gene, (b) probe specific for RFP2 gene or theircombinations.

In addition, the present invention provides uses of 1q as prognostic andtherapeutic targets in many cancers, including as a diagnostic,prognostic, or therapeutic target in myeloma. A person having ordinaryskill in this art would be able to detect aggressive disease bydetecting CKS1B, OPN3, and ASPM alone or in combination by DNA copyusing, but not limited to DNA arrays, interphase or metaphase FISH.Measuring gene expression levels by microarray or RT-PCR or the like, ormeasuring protein by tissue array, flow cytometry, immunohistochemistryor any other method of measuring protein content in tumor cells would bevaluable predictors of patient survival from various types of cancers.Since 1q amplification is a progressive event, continually testing foramplification of these genes during the disease management couldidentify the onset of aggressive behavior. Finally, since the CKS1B is asmall molecule with a powerful role in biology it represents a potentialtherapeutic target. A person having ordinary skill in this art would beable to manipulate this genes' copy number, its message through RNA1,antibody and or small molecule interference as a means of therapy.

Other and further aspects, features, and advantages of the presentinvention will be apparent from the following description of thepresently preferred embodiments of the invention. These embodiments aregiven for the purpose of disclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-B show Kaplan Meier survival curve analysis of event-freesurvival (FIG. 1B) and overall survival (FIG. 1A) in relation to CKS1Bexpression levels. The patient samples were grouped into quartiles basedon levels of gene expression. Q1 was the lowest quartile and Q4 was thehighest. Note the significant link between Q4 and poor prognosis.

FIG. 2A-2F shows overall survival analysis on patients with more than1.5 years follow-up. Patient samples were grouped into quartiles basedon levels of gene expression. Q1 was the lowest quartile and Q4 was thehighest. Note the significant link between poor prognosis and elevatedexpression of ASPM, OPN3 or CSK1B (upper panel). The power of survivalprediction was increased by grouping two or more of the three genes inthe analysis (lower panel).

FIG. 3A-3C shows ASPM, OPN3 or CSK1B can also predict event-freesurvival. FIG. 3D-3F shows that grouping two or more of the genes ASPM,OPN3 and CSK1B increases the power of predicting event-free survival.

FIG. 4 shows increase of CSK1B expression and copy number was associatedwith relapse.

FIGS. 5A-B show that CKS1B expression by myeloma plasma cells varies andthat high levels of expression of CKS1B define a high-risk myelomaentity. FIG. 5A shows box plots of log base 2-transformed Affymetrixsignal (y-axis) among 351 cases according to quartile expression levels(x-axis). FIG. 5B shows Kaplan-Meier plots of overall survival revealinferior outcome among the 88 patients with 4th quartile expressionlevels of CKS1B compared to the remaining 263 patients with quartile 1-3expression levels.

FIGS. 6A-D show that increased CKS1B expression is related to increasedCKS1B DNA copy number and the degree of DNA amplification is linked topoor survival. FIG. 6A shows metaphase fluorescence in situhybridization analysis of CKS1B at 1q21 (red signal) and ASPM at 1q31(green signal) performed on plasma cells from a patient with myeloma.Note the arrows pointing to tandem duplications of CKS1B and theirhigher prevalence relative to 1q31. FIG. 6B shows box plots of log base2-transformed Affymetrix Signal (y-axis) by CKS1B amplification (N=197).In box plots, the top, bottom, and middle lines corresponded to the75th, 25th and 50th percentiles, respectively, and the whiskers extendedto the nearest point not beyond 1.5 times the inter-quartile range, withobservations beyond these indicated by individual lines. A Wilcoxon ranksum test was used to compare Signal across copy number categories. FIG.6C shows a Kaplan-Meier plot of overall survival in the validationcohort depicts inferior outcomes among the 89 patients with CKS1Bamplification compared to the remaining 135, as determined by interphasefluorescence in situ hybridization. FIG. 6D shows the Kaplan-Meier plot,as in 6C, for the combined sample of 421 patients.

FIG. 7 shows that CKS1B expression increases in relapsed myeloma. CKS1BSignal for 32 paired diagnosis and relapse arrays. The quartile 4reference line was taken from the complete (N=351) sample of arrays atdiagnosis. Note that a majority of samples showed increased expressionat relapse; the most dramatic changes were observed in patients withquartile 1-3 expression levels at diagnosis. A Welch-modified, pairedt-test was used to compare log-scale Signal at diagnosis and relapse.

FIGS. 8A-E show that CKS1B mRNA correlates with nuclear protein levelsand inversely correlates with CDKN1B and siRNA to CKS1B can increase p27levels and reduce cell proliferation. FIG. 8A shows CKS1B and FIG. 8Bshows CDKN1B (CDKN1B) gene expression signal in 1000 unit increments isplotted on the y-axis. Primary myelomas with CKS1B expression inquartile 1 (n=13) and quartile 4 (n=14) and myeloma cell lines (n=7)were grouped and plotted from left to right along the x-axis. Each barrepresented a sample and the height indicated the level of geneexpression in the sample. Western blot analysis of nuclear proteinextracts for CKS1B (FIG. 8C), phospho-thr-187-CDKN1B (FIG. 8D), andHistone 1A (loading control; FIG. 8E) from aliquots of same plasma cellsused in 8A and 8B. Samples were ordered from left to right in the exactsame order in all panels.

The foregoing will be apparent from the following more particulardescription of example embodiments of the invention, as illustrated inthe accompanying drawings in which like reference characters refer tothe same parts throughout the different views. The drawings are notnecessarily to scale, emphasis instead being placed upon illustratingembodiments of the present invention.

DETAILED DESCRIPTION OF THE INVENTION

A description of example embodiments of the invention follows.

The variability in survival among patients with myeloma can range frommonths to more than 15 years. Patients at highest risk are bestidentified by the presence or absence of an abnormal karyotype. However,this test only accounts for ˜15% of the variability in outcome. Thus,many patients who present with no cytogenetic abnormalities experiencerapid relapse and/or early death. To better define high-risk disease andalso potentially identify genetic mechanisms that give rise to this poorsurvival, gene expression patterns were analyzed in freshly isolatedplasma cells from 40 newly diagnosed myeloma patients who were thentreated with tandem stem cell transplants. Patients were separated intotwo groups of 20 each. Those in the “short-survival” group all diedwithin 900 days of initiation of therapy. Patients in the“long-survival” group survived more than 1,453 days. RNA from plasmacells was labeled and hybridized to the U133Plus2.0 microarrays. Theexpression value was transformed by log base 2 and each sample wasnormalized to give a mean of 0 and a variance of 1. Chi-square analysesand t-tests were used to identify genes whose expression patterns wereunique to each group.

A total of 1770 probe sets were significantly differentially expressedbetween the two groups (P<0.05). A total of 1,025 (58%) of the probesets were elevated in the short-survival group. An overwhelmingmajority, 290 of the 1,770 genes (19%), mapped to chromosome 1. Of the1,770 probe sets, 84 demonstrating a >2-fold difference in expressionwere further analyzed with Kaplan-Meier survival analyses. In this test,17 genes were highly significant (P<0.0001) (Table 1). Of the 17 genesidentified, 10 (59%) map to chromosome 1. Of these 10 genes, all 4 genesfrom the p arm were down-regulated while all 6 genes from the q arm wereup-regulated in the short-survival group.

It has been previously demonstrated that jumping 1q and amplification ofgenes from 1q21 represent common genetic lesions in myeloma.Fluorescence in situ hybridization analysis of BCL9 and IL-6R has shownthat these genes can define a 1q21 amplicon. However, BCL9 and IL-6Rwere not linked to disease outcome. The present invention found thatCKS1B, which is located very near the 1q21 amplicon, is over-expressedin myelomas and highly correlated with overall survival (FIG. 1A) andevent-free survival (FIG. 1B). CKS1B is an evolutionarily conservedprotein that interacts genetically and physically with cyclin-dependentkinases and promotes mitosis. Quantitative RT-PCR was used to confirmthe microarray results for this gene. Given the important role of CKS1Bin controlling mitosis, CKS1B over-expression, possibly as a result ofgene amplification, may impart a highly aggressive phenotype onmalignant plasma cells.

Using microarray correlative studies with 350 newly diagnosed cases withoverall survival longer or less than 2 years from start of therapy, itwas found that elevated expression of genes from chromosome 1q was aglaring feature of early death. Using statistical modeling, a three genemodel is disclosed herein that could capture >80% of all early deaths.These three genes all mapped to chromosome 1. The genes from 1 qtelomere to centromere are: OPN3 (1q43), ASPM (101.3) and CKS1B (1q21).The CKS1B chromosome map position, only 200 Kb telomeric of IL6R,suggests that this gene is the target of 1q21 amplification in myeloma.Moreover, given the frequent amplification of 1q in many cancers, it ispossible that CKS1B, alone or together with the other two genesidentified above, may be a ubiquitous marker/target for cancer ingeneral.

CKS1B And Cell Cycle Control

CKS1B was originally defined by their ability to bind CDK/cyclincomplexes. CKS1B is a highly conserved protein of 79 amino acids thathas two homologs in higher eukaryotes. The human orthologs canfunctionally substitute for CKS1 in yeast. Most genetic and biochemicaldata point to a mitotic role for CKS proteins. Loss of function of CKS1results in M phase arrest with condensed but unsegregated chromosomes,an extended spindle and elevated levels of Cdc2/cyclin B kinaseactivity. CKS1 also has a G1 function. Immunodepletion of CKS1 orthologXep9 from interphase egg extracts prevented entry into mitosis, whereasdepletion from mitotic extracts leads to M phase arrest with elevatedlevels of cyclin B and CDK1/cyclin B kinase activity. These datasuggests that CKS proteins may be required for both entry into andprogression through mitosis.

DNA synthesis is mediated by the action of the cyclin E/CDK2 complex,which is in turn negatively regulated by the cyclin-dependent kinaseinhibitor CDKN1B (Shen and Roberts, 1999). The small evolutionarilyconserved protein CKS1 is required for SCF^(Skp2)-mediatedubiquitinylation and proteasomal degradation of cyclin-dependent kinaseinhibitor CDKN1B (Ganoth et al., 2001; Spruck et al., 2001). CDKN1Bdegradation not only permits DNA replication but also ensures thecorrect progression of cells through S phase into mitosis (Nakayama etal., 2004) and Cks proteins interact with the proteasome to control theproteolysis of mitotic cyclins by way of regulating the transcriptionalactivity of CDC20 (Morris et al., 2003), a regulatory subunit of theanaphase-promoting complex/cyclosome ubiquitin ligase (Peters, 2002).Thus, CKS1 and the SCF^(Skp2)-CDKN1B-Cdk½ axis appear to be importantfor both DNA synthesis and mitosis (Pagano, 2004). The low CDKN1Bprotein levels in cancer cells, in the absence of gene mutations, hasprompted speculation that hyper-activation of CKS1B and/or SKP2, mayaccount for the low levels of CDKN1B (Slingerland and Pagano, 2000).Moreover, CKS1B also regulates G2 to M transition by controlling cyclinB degradation by APC.

CKS1B and Cancer

Results disclosed below identify CKS1B located at 1q21 as a strongcandidate gene for conferring poor prognosis in patients getting tandemstem cell transplants for their myeloma. Fluorescence in situhybridization analysis confirmed elevated expression of CKS1B;therefore, survival was directly related to CKS1B gene transcriptionactivity and copy number in newly diagnosed patients. There has been asuggestion that prior therapy and long latency results in amplificationevent. Young (<50 years) patients are as likely to present with elevatedCKS1B as old patients (>60 years). Data from 20 patients with baselineand relapse samples showed that CKS1B gene amplification and increasedexpression was increased in patients who had normal baseline values.These data suggest that CKS1B amplification can be present at diagnosisand linked to poor survival and can be amplified during the course offulminate relapse.

Primary numerical chromosome aberrations seen in multiple myelomakaryotypes apparently evolve over an extended period of time as thedisease remains a subclinical phenomenon (MGUS). In later stages ofprogressive multiple myeloma cytogenetic evolution takes place,resulting in acquisition of additional abnormalities usually involvingchromosome 1. Trisomy of chromosome 1 is seen in 40% of myelomakaryotypes, and trisomy of the long arm of chromosome 1q is common inmany cancers such as leukemia and lymphomas. Duplicated 1q might be asecondary mutations associated with disease progression. Trisomy of 1qhas also been linked to metastatic potential of colon and renal cellcarcinomas.

This is the first report indicating that the CKS1B gene may be anoncogene and that this oncogene plays a role in acquiring drugresistance and rapid death in myeloma. The frequency of this geneticdefect in myeloma and other cancers such as leukemia, lymphomas, breastcancer, colon cancer and prostate cancer suggests that CKS1Bamplification is a frequent mechanism by which tumors develop highlyproliferative and multi-drug resistant disease. Development of smallmolecule inhibitors of CKS1B may be a future therapeutic strategy, andCKS1B could be a powerful marker for initial staging and diseasefollow-up for prediction of imminent relapse by detecting CKS1Bamplification with techniques such as gene expression profiling,fluorescence in situ hybridization or immunohistochemistry. In additionto over-expression of a gene, reduced expression of RFP2 gene onchromosome 13q14 either alone or in combination with over-expression ofCKS1B gene may play a significant role in the diagnosis of multiplemyeloma.

In one embodiment of the present invention, there is provided a methodof determining the prognosis of a multiple myeloma patient, comprisingthe steps of: obtaining plasma cells from said patient, determining geneexpression of one or more genes from the group consisting of GNG10,PNPLA4, KIAA1754, AHCYL1, MCLC, EV15, AD-020, PARG1, CTBS, FUCA1, RFP2,FLJ20489, LTBP1, TRIP13, AIM2, SELI, SLC19A1, LARS2, OPN3, ASPM, CCT2,UBE2I, STK6. FLJ13052, FLJ12525, BIRC5, CKS1B, CKAP1, MGC57827,DKFZp7790175, PFN1, ILF3, IFI16, TBRG4, PAPD1, EIF2C2, MGC4308, ENO1,DSG2, EXOSC4, TAGLN2, RUVBL1, ALDOA, CPSF3, MGC15606, LGALS1, RAD18,SNX5, PSMD4, RAN, KIF14, CBX3, TMPO, DKFZP586LO724, WEE1, ROBO1, TCOF1,YWHAZ, MPHOSPH1 in the plasma cell, and comparing the expression levelof the gene(s) with expression level of the gene in a controlindividual, where reduced expression, overexpression of the gene ortheir combination compared to the gene expression levels in plasma cellof a control individual indicates that the patient would have a poorprognosis.

A patient having a poor prognosis is the one who is at risk ofdeveloping aggressive form of the disease, suffering from relapse orwill have a shorter life expectancy. Specifically, the reducedexpression of the gene, overexpression of the gene or their combinationin a patient after treatment predicts risk of relapse in the patientafter treatment. Examples of the treatment that such a patient wouldhave undergone is high dose chemotherapy and autologous peripheral bloodstem cell transplantation. Examples of the genes with a reducedexpression although not limited to include GNG10, PNPLA4, KIAA1754,AHCYL1, MCLC, EV15, AD-020, PARG1, CTBS, FUCA1, RFP2, FLJ20489 or LTBP1.Furthermore, examples of the genes that are overexpressed although notlimited to include TRIP13, AIM2, SELI SLC19A1, LARS2, OPN3, ASPM, CCT2,UBE2I, STK6. FLJ13052, FLJ12525, BIRC5, CKS1B, CKAP1, MGC57827,DKFZp7790175, PFN1, ILF3, IFI16, TBRG4, PAPD1, EIF2C2, MGC4308, ENO1,DSG2, EXOSC4, TAGLN2, RUVBL1, ALDOA, CPSF3, MGC15606, LGALS1, RAD18,SNX5, PSMD4, RAN, KIF14, CBX3, TMPO, DKFZP586LO724, WEE1, ROBO1, TCOF1,YWHAZ or MPHOSPH1. Specifically, the gene that is overexpressed is CKS1Bgene and the gene with reduced expression is the RFP2 gene.Additionally, the control individual is a normal, healthy individual oran individual diagnosed with multiple myeloma lacking overexpression ofthe gene, reduced expression of the gene or a combination thereof.Moreover, the gene expression may be determined by DNA microarray orRT-PCR.

In another embodiment of the present invention, there is provided amethod of determining the prognosis of a multiple myeloma patient,comprising the steps of: obtaining plasma cell from the patient, anddetermining copy number of one or more genes discussed supra, wherein adecreased copy number, increased copy number or a combination thereofcompared to copy number in a plasma cell of a control individualindicates that the patient would have poor prognosis. As discussedsupra, a decreased copy number, increased copy number of the gene ortheir combination in a patient after treatment predicts risk of relapseafter treatment. The type of treatment is the same as discussed supra.

Additionally, examples of the genes with decreased copy is the same asthe genes with reduced expression whereas examples of the gene withincreased copy number is the same as the genes with overexpression.Furthermore, a preferred gene with an increased copy number is the CKS1Bgene and a preferred gene with a reduced copy number is the RFP2 gene.The control individual in this method is a normal healthy individual oran individual diagnosed with multiple myeloma lacking the decreased copynumber, increased copy number of the gene or their combination.Furthermore, the copy number of the gene is determined by fluorescencein situ hybridization. In a further related embodiment of the presentinvention is a kit comprising; probe(s) specific for one or more of thegenes discussed supra.

In a yet another embodiment of the present invention, there is provideda method of determining the risk of developing a disease-related eventfor a cancer patient. Such a method comprises the steps of: obtainingbiological samples from the patient, and determining gene expressionlevels, copy number or their combination of one or more genes belongingto the group discussed above as being overexpressed, whereoverexpression, increased copy number of the gene or a combinationthereof compared to the gene expression levels, copy number of theircombination in a normal individual indicates that the patient would havean increased risk of developing a disease-related event. Representativeexamples of the gene that is overexpressed or has an increased copynumber is OPN3, CKS1B or ASPM gene.

Generally, the disease-related event consists of death, progression toan aggressive form of the disease and relapse. Additionally, the cancerpatient may be an individual with 1q21 amplification. Such an individualmay be a multiple myeloma, breast cancer, colon cancer or prostatecancer patient. Moreover, the control individual is the same as in themethods described supra. Furthermore, the gene expression level or copynumber is determined either before or after treatment of the patient.The type of treatment, the method used to determine the gene expressionlevel and copy number is the same as discussed supra. Additionally, thegene expression level is determined at the protein level. Examples ofsuch methods although not limited to include flow cytometry,immunohsitochemistry and tissue array.

In another embodiment of the present invention, there is provided amethod of treating a cancer patient having overexpression of CKS1B geneor CKS1B gene product, comprising the step of administering to thepatient an agent that downregulates the expression of the CKS1B gene orthe CKS1B gene product. Such a patient may be an individual with 1q21amplification. Furthermore, such an individual may be a multiplemyeloma, a breast cancer, a colon cancer or a prostate cancer patient.Examples of agents that downregulate the expression of the CKS1B geneare not limited to but include RNA mediated interference or a peptidenucleic acid (PNA). Examples of agents that downregulate the expressionof CKS1B gene are not limited to but include anti-sense oligonucleotide,antibody or a small molecule inhibitor that are well known to one ofskill in the art.

In yet another embodiment of the present invention, there is provided amethod of treating an individual having high-risk multiple myeloma,comprising administering to the individual pharmaceutically effectiveamounts of a compound that downregulates the expression of CKS1B gene orCKS1B gene product and a vector comprising DNA sequence encoding RFP2gene. The examples of compounds that down regulate the expression ofCKS1B gene or its product are the same as discussed supra.

In still yet another embodiment of the present invention, there isprovided a kit, comprising; (a) probe specific for CKS1B gene, (b) probespecific for RFP2 gene, or their combinations.

The present examples, along with the methods, procedures, treatments,molecules, and specific compounds described herein are presentlyrepresentative of preferred embodiments and are not meant to limit thepresent invention in any fashion. One skilled in the art will readilyappreciate that the present invention is well adapted to carry out theobjects and obtain the ends and advantages mentioned, as well as thoseobjects, ends and advantages inherent herein. Changes therein and otheruses which are encompassed within the spirit of the invention as definedby the scope of the claims will occur to those skilled in the art.

Example 1

Overall Survival Linked to Gain of Chromosome 1 Genes

This example discloses gene expression profiling data identifying geneswhose expression in malignant plasma cells of newly diagnosed myelomapatients is significantly correlated with early death in patientstreated with tandem stem cell transplants.

FIG. 2A-2F shows overall survival analysis on patients with more than1.5 years follow-up. Patient samples were grouped into quartiles basedon levels of gene expression. Q1 is the lowest quartile and Q4 is thehighest. There was significant link between poor prognosis and elevatedexpression of ASPM, OPN3 or CSK1B (FIG. 2A-2F, upper panel). The powerof survival prediction was increased by grouping two or more of thesethree genes in the analysis (FIG. 2A-2F, lower panel).

These three genes capable of predicting overall survival can also beused to predict event-free survival (FIG. 3A-3C), and the power ofprediction was increased by grouping two or more of the three genes inthe analysis (FIG. 3D-3F). FIG. 4 shows increase of CSK1B expression andcopy number was associated with relapse.

While this invention has been particularly shown and described withreferences to example embodiments thereof, it will be understood bythose skilled in the art that various changes in form and details may bemade therein without departing from the scope of the inventionencompassed by the appended claims.

TABLE 1 Seventeen Genes Whose Expression Levels Predict Early Death FromMultiple Myeloma Probe Set Gene Symbol Chromosome 1565951_s_at OPN3 1q43200850_s_at AHCYL1 1p12 201897_s_at CKS1B 1q21.2 201921_at GNG10 9q32202345_s_at FABP5 8q21.13 202729_s_at LTBP1 2p22-p21 206513_at AIM2 1q22208540_x_at S100A11 1q21 209717_at EVI5 1p22 210427_x_at ANXA2 15q21-q22213704_at RABGGTB 1p31 219918_s_at ASPM 1q31 222495_at AD-020 1p13.3224847_at CDK6 7q21 227525_at GLCCI1 7p22.1 230100_x_at PAK1 11q13-q14242488_at 1q43

Example 2

Gene Expression Profiling to Identify Candidate Genes as Diagnostic,Prognostic and Potential Targets of High-Risk Phenotype

As discussed above, global gene expression profile identified geneswhose over-expression or lack of expression could be useful for stagingand performing a disease follow-up for multiple myeloma and othercancers. This gene profiling was also used to identify genes whoseabnormal expression might cause high-risk phenotype of myeloma.

(A) Subjects

668 newly diagnosed patients with symptomatic or progressive multiplemyeloma were enrolled in the study, which included 2 cycles of bloodstem cell-supported high-dose melphalan (200 mg/m2) (Shaughnessy et al.,2003). A subset of 575 patients with available genetic measurements, asdescribed below, constituted the sample for this analysis. Their medianfollow-up was 30 months. There were 185 progression or death events and128 deaths. Patient characteristics were as follows: 20% were 65 yearsor older, 31% had beta-2-microglobulin levels >=4 mg/L, 55% hadC-reactive protein levels >=4 mg/L; 22% presented with hemoglobin values<=10 g/dL, 10% with creatinine values >=2 mg/dL; LDH was elevated (>=190IU/L) in 30%, albumin decreased (<3.5 g/dL) in 15%; cytogeneticabnormalities were detected in 33%. The median follow-up for survival inthis subset was 22 months and there were 98 events and 64 deaths.

(B) Gene Expression Profiling

Gene expression profiling, using the Affymetrix U133Plus2.0 microarray,was performed on CD138-enriched plasma cells isolated from 351consecutive patients, as previously described (Zhan et al., 2002).

(C) Fluorescence In-Situ Hybridization (Fish)

Bacterial artificial chromosomes encompassing CKS1B at 1q21(RP11-307C12) and ASPM (RP11-32D17) at 1q31 were purchased from BAC/PACResources (Oakland, Calif.) and directly labeled with Spectrum-Green orSpectrum-Red (Vysis Inc, Downers Grove, Ill.). Metaphase fluorescence insitu hybridization was performed as previously described (Sawyer et al.,2005). The probes were confirmed to map to the 1q21 and 1q31 bands usingmetaphase spreads from normal human lymphocytes. Triple color interphasefluorescence in situ hybridization analyses of chromosomes 13 (D13531)and 1q21 (CKS1B) copy number were performed as described (Shaughnessy etal., 2000) in a subset of 421 patients (145 events and 100 deaths,follow-up of 31 months); deletion 13q was scored positive when >=80% ofclonal cells exhibited loss of a signal at 13q14 as described (McCoy etal., 2003). Of these 421 patients, 197 were among those with microarraysand 224 were not.

(D) Western Blotting

Nuclear protein was isolated from an aliquot of CD138 enriched plasmacells that were also analyzed by microarray. Western blotting wascarried using the WesternBreeze® Chemiluminescent immunodetectionprotocol as described (Invitrogen, Carlsbad, Calif.). The antibodies toCKS1B and phospo-thr-187-CDKN1B were purchased from Zymed LaboratoriesInc, (South San Francisco, Calif.) and anti-Histone 1A was purchasedfrom Upstate Biotechnology (Charlottesville, Va.).

(E) Statistical Analysis

The sample of 351 Affymetrix U133Plus2.0 microarrays were preprocessedusing MAS5.01 software and normalized using conventional MAS5.01scaling, as detailed in the Supplemental Methods. Log rank tests forunivariate association with disease-related survival were performed foreach of the 54,675 ‘Signal’ summaries. Specifically, log rank tests wereperformed for quartile 1 vs. quartiles 2-4 and quartile 4 vs. quartiles1-3, in order to identify under- and over-expressed genes, respectively.A false discovery rate cut-off of 2.5% was applied to each list oflog-rank P-values (Storey et al., 2003), yielding 19 under- and 51over-expressed probe sets. For all 70, extreme quartile membership (Q1or Q4) was associated with a higher risk of disease-related death. Allother EFS and survival outcomes in this analysis were overall (i.e. notdisease-related). The Kaplan-Meier method was used to estimateevent-free and overall survival distributions and log rank tests wereused to test for their equality across groups. Chi-square tests andFisher's exact tests were used to test for the independence ofcategories. Multivariate proportional hazards regression was used toadjust the effects of CKS1B expression and amplification for otherpredictors, and the proportions of observed heterogeneity explained bythe combined predictors (i.e. R2) were computed (O'Quigley and Xu etal., 2001). The statistical package R version 2.0 (R Development CoreTeam, 2004) was used for this analysis.

Microarray data for the 351 patients has been deposited in the NIH GeneExpression Omnibus under accession number GSE2658. Note that an analysisof baseline samples for 174 of the same patients was previously reported(De Vos et al., 2002) using Affymetrix U95Av2 microarrays. These sampleswere again hybridized to U133Plus2.0 microarrays for the currentanalyses.

(F) Fish-Based CKS1B Amplification Index

A conventional, laboratory-defined cutoff of 20% for the proportion ofclonal plasma cells with 3 signals or >=4 signals was used for tests ofassociation between expression and amplification (FIG. 6B and Table 5)and for validation of the association between amplification and overallsurvival (FIGS. 6C-D). Hypothesizing that 2 or more extra copies wouldconfer additional risk compared to 1 extra copy, the multivariateanalysis of overall survival (Table 4A) estimated separate effect sizesfor the 3 signal proportion and the >=4 signal proportion. These effectsizes were used to define the amplification index as a weighted sum:(0.34*% 3 Copies+0.66*%>=4 Copies)/0.66. The index is scaled so that itincreases by one for each unit increase in the proportion with >=4signals. The index is 0 for patients with <=2 signals in 100% of clonalcells, 51.5% for patients with 3 signals in 100%, and 100 for patientswith >=4 signals in 100%. The full range was observed in these patients.A cutoff for the index of >=46 minimized the unadjusted log rank P-valuefor survival in the 421 patient subset (i.e. an optimal cutoff). Notethat all cutoffs for the index between 3 and 88 had P<0.003.

(G) Genetic Sub Groups

Nearly 50% of newly diagnosed myelomas contain one of five recurrentchromosomal translocations that result in the hyper-activation of MAF,MAFB, FGFR3/MMSET, CCND3, CCND1 (Kuehl et al., 2002) with divergentprognoses (Fonseca et al., 2004), detectable as “spiked” expression bymicroarray analysis (Valk et al., 2004). Genetic subgroups wereclassified based on presence or absence of these translocation spikes.Patients were also classified within the context of metaphasecytogenetics as having normal karyotypes (originating in normalhematopoietic cells in case of hypoproliferative myeloma) or as havinghyperdiploid, hypodiploid or “other” cytogenetic abnormalities. “Other”is defined as an abnormal metaphase karyotype, i.e. structural and/ornumeric changes, with a diploid modal chromosome number. Thus, differentfrom the Paris workshop (Fonseca et al., 2004), non-translocationentities were defined by metaphase rather than interphase cytogenetics.

(I) Microarray Analysis

Affyrnetrix MAS5.01 preprocessed ‘Signal’ summaries were usedexclusively for this analysis, with MAS5.01 array normalizationperformed by scaling the 2% trimmed mean of each array's probe setsignals to equal 500. To select focus genes, a single criterion was usedfor both probe set filtering and significance analysis as an outgrowthof the particular experimental design. Rather than comparing continuousexpression levels across pre-defined categories, as is often the case,the design called for comparing the distribution of earlydisease-related death (median follow-up <2 years) across quartiles ofthe expression distribution. The design was informed by the biologicalhypothesis that poor-prognosis genes which are “switched” off or on maybe associated with expression in the lower or upper quartile of thesample, respectively. Log rank tests for disease-related survivaldifferences across Q1 vs. other and Q4 vs. other were performed for all54,675 probe set signals, with the single restriction that the samplecontained sufficient unique signal values for the probe set, a conditionmet by all (i.e. a minimum of 79 unique values). Among the 70 probe setsdeclared significant for under- or over-expression, the minimum numberof unique values was 323 (30th percentile of the 54,675) and the medianwas 346 (83rd percentile). The minimum sample variance of the log base 2signals was 0.13 (0.6th percentile) and the median was 0.52 (29thpercentile). The minimum fold change over the signal range was 2.13(0.4th percentile) and the median was 5.26 (40th percentile).Examination of the expression distributions of probes sets declaredsignificant suggested no reason why any of them should be “filtered” outby minimum variance or fold change filters, particular since the largestlog rank P-value was 0.00003. Significance analysis was performed bycomputing estimates of the false discovery rates that correspond tospecified P-value cutoffs, as described by Storey and Tibshirani(Shaughnessy et al., 2003). The 70 gene list is based upon P-valuecutoffs with estimated false discovery rates of 2.5% for the under- andover-expressed P-value lists.

Example 3 Results of the Global Gene Expression Profiling

On a molecular basis to identify genes that might contributed tohigh-risk myeloma, gene expression profiles of purified plasma cellswere correlated with disease-related and overall survival in 351 newlydiagnosed patients treated with 2 cycles of high-dose melphalan.

Using log rank tests, 70 genes were identified for which fourth or firstquartile membership was correlated with a high incidence ofdisease-related death (Table 2). Although 10% of the genes on themicroarray were derived from chromosome 1, 30% of the retained geneswere derived from this chromosome (P<0.0001); 9 of 51 quartile 4 genesmapped to chromosome arm 1q and 2 to arm 1p whereas 9 of 19 quartile 1genes mapped to chromosome arm 1p and none on arm 1q (Table 3). Theover-representation of 1q genes among the list of 70 and the observationthat amplification of 1q21 was associated with progression and poorprognosis in myeloma (Smadja et al., 2001; Sawyer et al., 2005; Philipet al., 1980) justified a focus on this region in search for a molecularbasis of high-risk myeloma: 2 genes (PSMD4 and CKS1B) map to 1q21, amongwhich CKS1B quartile 4 membership was most strongly associated withsurvival in unadjusted log rank tests (Table 2).

TABLE 2 A. Quartile 4 FDR 2.5% gene probe sets -- rank correlations with1q21 amplification index, CKS1B and PC labeling index and adjustedP-values for associations with overall survival CKS1B AmplificationAdjusted Rank Index CKS1B PCLI Survival (Q4) Chromosome Probe set Symbolr^(†) r^(‡) r* P-value^(a) 1 8q21.13 202345_s_at NA 0.20 0.22 0.001 2Xp22.2- 1555864 _(—) s _(—) at NA 0.34 0.47 0.007 p22.1 3 5p15.33 204033_(—) at TRIP13 0.19 0.45 0.20 0.001 4 1q22 206513_at AIM2 0.15 0.130.089 5 2p24.1 1555274_a_at SELI 0.28 0.31 0.001 6 21q22.3 211576_s_atSLC19A1 0.17 0.23 0.007 7 3p21.3 204016_at LARS2 −0.18 0.002 8 1q431565951_s_at OPN3 0.36 0.36 0.007 9 1q31 219918 _(—) s _(—) at ASPM 0.360.64 0.17 0.010 10 12q15 201947 _(—) s _(—) at CCT2 0.23 0.43 0.13 0.00411 16p13.3 213535_s_at UBE2I 0.38 0.022 12 20q13.2- 204092 _(—) s _(—)at STK6 0.31 0.51 0.19 0.044 q13.3 13 1p36.33- 213607_x_at FLJ130520.150 p36.21 14 Xq12- 208117_s_at FLJ12525 0.34 0.006 q13 15 17q25210334_x_at BIRC5 0.20 0.36 0.14 0.110 16 3q27 204023 _(—) at NA 0.290.62 0.16 0.072 17 1q21.2 201897 _(—) s _(—) at CKS1B 0.50 1.00 0.150.007 18 19q13.11- 216194_s_at CKAP1 0.24 0.38 0.001 q13.12 19 1q21225834 _(—) at MGC57827 0.39 0.66 0.23 0.140 20 19q13.12 238952_x_atDKFZp779O175 0.11 0.009 21 17p13.3 200634 _(—) at PFN1 0.30 0.41 0.00222 19p13.2 208931_s_at ILF3 0.22 0.22 0.220 23 1q22 206332_s_at IFI160.30 0.32 0.13 0.003 24 7p14- 220789_s_at TBRG4 0.13 0.17 0.009 p13 2510p11.23 218947_s_at PAPD1 0.31 0.30 0.150 26 8q24 213310_at EIF2C2 0.280.37 0.031 27 3q12.1 224523_s_at MGC4308 0.17 0.24 0.14 0.038 28 1p36.3-201231_s_at ENO1 0.23 <0.001 p36.2 29 18q12.1 217901_at DSG2 0.15 0.00530 6q22 226936 _(—) at NA 0.15 0.52 0.17 0.027 31 8q24.3 58696_at EXOSC40.20 0.330 32 1q21- 200916 _(—) at TAGLN2 0.47 0.52 0.120 q25 33 3q21201614_s_at RUVBL1 0.16 0.14 0.023 34 16q22- 200966_x_at ALDOA 0.21 0.280.001 q24 35 2p25.1 225082_at CPSF3 0.39 0.073 36 1q43 242488_at NA 0.180.27 0.14 0.090 37 3q12.3 243011_at MGC15606 0.27 0.004 38 22q13.1201105_at LGALS1 0.31 0.051 39 3p25- 224200 _(—) s _(—) at RAD18 0.170.41 0.14 0.040 p24 40 20p11 222417_s_at SNX5 0.085 41 1q21.2 210460_(—) s _(—) at PSMD4 0.58 0.59 0.13 0.067 42 12q24.3 200750 _(—) s _(—)at RAN 0.22 0.40 0.056 43 1pter-q31.3 206364 _(—) at KIF14 0.41 0.570.25 0.019 44 7p15.2 201091_s_at CBX3 0.14 0.20 0.16 0.150 45 12q22203432 _(—) at TMPO 0.32 0.59 0.18 0.007 46 17q24.2 221970 _(—) s _(—)at DKFZP586L0724 0.27 0.47 0.081 47 11p15.3- 212533 _(—) at WEE1 0.200.54 0.13 0.056 p15.1 48 3p12 213194_at ROBO1 0.150 49 5q32-q33.1244686_at TCOF1 0.120 50 8q23.1 200638_s_at YWHAZ 0.26 0.23 0.012 5110q23.31 205235 _(—) s _(—) at MPHOSP1 0.40 0.16 0.050 B Quartile 1 geneprobe sets satisfying FDR 2.5% cutoff CKS1B Amplification Adjusted RankIndex CKS1B PCLI Survival (Q1) Chromosome Probe set Symbol r^(†) r^(‡)r* P-value^(a) 1 9q31.3 201921_at GNG10 −0.20 −0.30 0.600 2 1p13227278_at NA −0.12 0.900 3 Xp22.3 209740_s_at PNPLA4 0.029 4 20q11.21227547_at NA −0.29 −0.28 −0.15 0.630 5 10q25.1 225582_at KIAA1754 −0.21−0.32 0.003 6 1p13.2 200850_s_at AHCYL1 −0.13 0.019 7 1p13.3 213628_atMCLC −0.30 −0.28 −0.15 0.440 8 1p22 209717_at EVI5 −0.33 −0.29 −0.160.870 9 1p13.3 222495_at AD-020 −0.30 −0.24 −0.20 0.920 10 6p21.311557277_a_at NA −0.11 0.460 11 1p22.1 1554736_at PARG1 −0.20 −0.11 0.28012 1p22 218924_s_at CTBS −0.16 −0.11 −0.13 0.460 13 9p13.2 226954 _(—)at NA −0.22 −0.40 0.090 14 1p34 202838_at FUCA1 −0.17 −0.23 0.066 1513q14 230192_at RFP2 −0.28 −0.18 0.880 16 12q13.11 48106_at FLJ20489−0.23 −0.23 −0.11 0.300 17 11q13.1 237964_at NA −0.16 −0.20 0.044 182p22-g21 202729_s_at LTBP1 −0.24 −0.21 0.097 19 1p13.1 212435_at NA−0.21 −0.21 −0.11 0.034 ^(†)Correlation between each gene's log-scaleexpression and the CKS1B amplification index (N = 197, all patients withboth GEP and FISH 1q21). Blank cells correspond to correlations with P >0.05. ^(‡)Correlation between each gene's log-scale expression and CKS1Blog-scale expression (N = 351, all patients with GEP). Rows with CKS1B|r| >=0.4 are formatted bold. Correlation between each gene's log-scaleexpression and the PCLI (N = 305, 46 patients are missing PCLI).^(a)Multivariate proportional hazards regression of overall survival onextreme quartile expression (Q1 or Q4) for each gene, adjusted for FISH13 80%, cytogenetic abnormalities, B2M > 4, CRP > 4, ALB < 3.5 and PCLI(N = 277, 74 patients are missing at least one measurement).

TABLE 3 Chromosome distribution of 2.5% FDR gene probe sets U133Plus2.0Q1 Q4 Combined Chromo- Number Number Number Number p some of Genes % ofGenes % of Genes % of Genes % value* 1 3,659 9.9 9 47.4 12 23.5 21 30.0<0.0001 2 2,522 6.9 1 5.3 2 3.9 3 4.3 3 2,116 5.8 0 0.0 7 13.7 7 10.0 41,456 4.0 0 0.0 0 0.0 0 0.0 5 1,718 4.7 0 0.0 2 3.9 2 2.9 6 2,005 5.4 15.3 1 2.0 2 2.9 7 1,798 4.9 0 0.0 2 3.9 2 2.9 8 1,311 3.6 0 0.0 4 7.8 45.7 9 1,463 4.0 2 10.5 0 0.0 2 2.9 10 1,444 3.9 1 5.3 2 3.9 3 4.3 112,069 5.6 1 5.3 1 2.0 2 2.9 12 1,927 5.2 1 5.3 3 5.9 4 5.7 13 730 2.0 15.3 0 0.0 1 1.4 14 1,195 3.2 0 0.0 0 0.0 0 0.0 15 1,152 3.1 0 0.0 0 0.00 0.0 16 1,507 4.1 0 0.0 2 3.9 2 2.9 17 2,115 5.7 0 0.0 3 5.9 3 4.3 18582 1.6 0 0.0 1 2.0 1 1.4 19 2,222 6.0 0 0.0 3 5.9 3 4.3 20 1,072 2.9 15.3 2 3.9 3 4.3 21 468 1.3 0 0.0 1 2.0 1 1.4 22 906 2.5 0 0.0 1 2.0 11.4 X 1,273 3.5 1 5.3 2 3.9 3 4.3 Y 80 0.2 0 0.0 0 0.0 0 0.0 m 5 0.0 00.0 0 0.0 0 0.0 36,795 19 51 70 Unknown 17,880 54,675 *An exact test forbinomial proportions was used to compare the proportion of retainedprobe sets mapping to chromosome 1 to the proportion for the entirearray.

The log-scale expression levels of proliferation-associated genes tendedto have high correlations with CKS1B (Table 2). In addition, 25 of 29(86%) genes, significantly correlated with the plasma cell labelingindex, were strongly correlated with CKS1B, suggesting that this geneparticipated in a proliferation signaling network in patients with highrisk disease. CKS1B was an independent predictor of overall survivalafter adjustment for chromosome 13 deletion by interphase FISH,metaphase cytogenetic abnormalities, clinical prognostic factors andlabeling index (P=0.007, Table 2, last column, row 17). AdjustedP-values are provided for the other 69 genes for comparison, and it wasevident that few other chromosome 1 genes are both strong independentpredictors of survival, proliferation, and CKS1B gene amplification.

Although the median age of the present cohort was 57, younger than themedian age at diagnosis, the 25% between 64 and 76 were sufficient toconsider whether age modified the effect of CKS1B over-expression oramplification in the multivariate analyses in Tables 2 and 4b,respectively. As a continuous variable, age was not a significantmodifier of CKS1B's effect on survival in either analysis (P=0.37, HR1.03, for CKS1B expression and P=0.81, HR 0.99, for amplification), withthe strongest effect corresponding to an estimated 3% higher hazard foran additional 1 year in age (results are similar for EFS). Additionally,there was a slightly higher prevalence of CKS1B amplification amongpatients 65 and older (P=0.2). It was speculated that genes associatedwith the 1q21-mediated proliferation pathway dominated as univariatepredictors of disease-related survival in early follow-up. Genes relatedto other genetic lesions, such as FGFR3/MMSET, MAF and MAFB ranked belowthe 70, but might appear at higher false discovery rates.

TABLE 4 Multivariate proportional hazards analysis^(†) (n = 369) A.Event-Free Survival Survival Cumu- Cumu- lative lative % HR 1. r² HR Pr² CKS1B 1.009 0.002 0.160 1.011 0.002 0.219 Ampli- fication Index(0-100) FISH 25.5 1.786 0.006 0.224 1.879 0.014 0.308 Chromosome 13Deletion Abnormal 35.0 1.875 0.001 0.272 2.298 <0.001 0.393 KaryotypeBeta-2- 35.8 1.478 0.046 0.305 1.396 0.170 0.422 micro- globulin >= 4mg/L C-reactive 63.4 1.533 0.028 0.320 1.586 0.055 0.448 protein >= 4mg/L Albumin < 16.5 1.660 0.019 0.336 1.698 0.044 0.461 3.5 g/dL Events/127 84 Deaths B. Event-Free Survival Survival Cumu- Cumu- lative lative% HR P r² HR P r² CKS1B 32.5 1.68 0.008 0.132 2.12 0.001 0.207 Ampli-fication Index >= 46 FISH 25.5 1.74 0.010 0.204 1.83 0.020 0.293Chromosome 13 Deletion Abnormal 35.0 1.94 <0.001 0.257 2.33 <0.001 0.383Karyotype Beta-2- 35.8 1.52 0.033 0.293 1.43 0.140 0.417 micro-globulin >= 4 mg/L C-reactive 63.4 1.49 0.038 0.312 1.56 0.060 0.443protein >= 4 mg/L Albumin < 16.5 1.69 0.016 0.331 1.73 0.035 0.455 3.5g/dL Events/ 127 84 Deaths ^(†)369 of 421 patients with CKS1Bamplification measurements had complete measurements for this analysis)a) Multivariate proportional hazards analysis with the continuous CKS1BThus, based on its well-documented role in regulating cell cycleprogression, its chromosome map location, link to myeloma cellproliferation and patient survival, CKS1B was considered a candidategene, the inappropriate expression of which might promote an aggressivephenotype.

As was true for all the gene transcripts listed in Table 2, CKS1B levelswere strongly correlated with clinical outcome (FIG. 5): 25 deaths hadoccurred among 88 patients with quartile 4 expression levels compared toonly 39 among the 263 patients with quartile 1-3 levels (p<0.0001, falsediscovery rate, 2.5%); this was also true for event-free survival (34 of88 in the quartile 4 cohort had experienced an event compared to 64 of263 in the remainder; p<0.0001). Levels of SKP2, the CKS1B partner gene,were uniformly high and not significantly associated with survival(P=0.3). Additionally, interphase FISH analysis revealed 3 or morecopies of CKS1B in 46% among 197 cases with concurrent gene expressiondata. Expression levels were significantly linked to CKS1B copy number(FIG. 6B). Conversely, amplification increased in frequency as CKS1Bexpression levels increased from quartile 1 to quartile 4 (P<0.0001,Table 5). Examination of CKS1B gene amplification in the context ofexpression levels of the 70 genes (Table 2) revealed, as expected,correlations with genes on chromosome band 1q21 but, importantly, alsowith genes linked to cell proliferation not mapping to 1q21.

TABLE 5 Relationship between CKS1B gene expression quartiles and CKS1Bamplification by interphase fluorescence in-situ hybridization in newlydiagnosed myeloma. CKS1B Expression ^(†) # AMPLIFIED % AMPLIFIEDquartile 1^(‡) 9 20% n = 44 quartile 2 12 28% n = 43 quartile 3 26 51% n= 51 quartile 4 44 75% n = 59 total 197 91 46% ^(†) P < 0.0001.Amplification is defined as >=20% of cells with 3 or >=4 CKS1B signals,for validation in conjunction with FIG. 2c-d, as described in theMethods. Other tables use the CKS1B amplification index and its optimalcutoff. ^(‡)Quartile assignments based upon 351 patients with GEP

All myeloma cell lines expressed elevated levels of CKS1B and ASPM,mapping to 1q31 and in the list of 51 over-expressed genes linked tooutcome in this analysis. Metaphase FISH for CKS1B and ASPM revealed 3-to 8-copies of CKS1B in 21 cell lines, whereas ASPM was amplified (3- to6-copies) in only 16 cell lines (data not shown). Metaphase FISH of aprimary myeloma (FIG. 6A) provided clear evidence of CKS1B amplificationin the absence of ASPM amplification. Thus, even though overexpressionof both genes was linked to survival and both genes map to the samechromosome band, CKS1B was more frequently amplified in myeloma thanASPM.

Next, the relationship between cytogenetic abnormalities involvingchromosome 1q and CKS1B FISH was examined. In 414 primary cases withboth abnormal cytogenetics and interphase FISH data for CKS1Bamplification, CKS1B amplification was observed in 16 of 17 cases (94%)with 1q gain by cytogenetics, while CKS1B amplification was observed byinterphase FISH in 61 of 112 cases lacking gross evidence of 1qabnormalities in spite of the presence of abnormal metaphasecytogenetics (data not shown). Taken together these data suggested thatCKS1B amplification was not simply mirroring chromosome 1 trisomy.

The BAC clone used to evaluate CKS1B gene copy number also measured thecopy number of PBXIP1 (mapping centromeric to CKS1B) and PB591, LENEP,ZFP67, FLJ32934, ADAM15 and EFNA4 (all mapping telomeric to CKS1B). Inexamining the relationship between gene copy number and the expressionlevels of these genes (Table 6), RNA expression was most stronglycorrelated with DNA copy number in the case of CKS1B. Importantly, noneof the other genes mapping to this BAC were among the 70 linked to shortsurvival. Moreover, the expression of candidate genes BCL9, MCL1, IL6R,and RAB25, that did not map to the BAC clone, but that did map to 1q21,were not linked to survival in this analysis (data not shown).

TABLE 6 Relationship of quartile 4 gene expression to amplification forgenes located on bacterial artificial chromosome (BAC) used to measure1q21 amplification Amplified* Not (Amplification. Ampli- Log AmplifiedIndex. >=46) fication Rank n/ n/ P- Index P- Symbol 129 (%) 68 (%)Value^(†) r^(‡) Value^(a) PBXIP1 24 (18.6) 28 (41.2) 0.0012 0.29 0.5285CKS1B 20 (15.5) 39 (57.4) <0.0001 0.50 0.0002 PB591 23 (17.8) 38 (55.9)<0.0001 0.43 0.0873 LENEP 31 (24.0) 18 (26.5) 0.8389 0.03 0.6507 ZFP6727 (20.9) 29 (42.6) 0.0023 0.34 0.8717 FLJ32934 28 (21.7) 11 (16.2)0.4606 −0.02 0.6207 ADAM15 23 (17.8) 29 (42.6) 0.0003 0.23 0.2808 EFNA426 (20.2) 23 (33.8) 0.0528 0.21 0.3212 *The 0-100 scale CKS1Bamplification index is a weighted sum of the proportions of clonal cellswith 3 copies of CKS1B and >=4 copies of CKS1B, defined by (.34 * %3copies + .66 * % >=4 copies)/.66. ^(†)For a test of the independence ofamplification and 4th quartile membership (N = 197). ^(‡)Correlationbetween each gene's expression and the 0-100 scale CKS1B amplificationindex^(.) ^(a)Log rank test for association of Q4 membership and overallsurvival (N = 351, 64 deaths)

Furthermore, the association of CKS1B amplification with survival andevent-free survival was validated in a cohort of 224 patients lackingmicroarray data. CKS1B amplification levels were inversely correlatedwith both event-free survival (P<0.0001) and overall survival (P<0.0001,FIG. 6C). These effects were also observed when all 421 patients wereconsidered (event-free survival, p<0.0001; overall survival, P<0.0001,FIG. 6D).

Next, multivariate proportional hazards analyses were performed usingthe 369 patients with both CKS1B amplification data and all additionalrisk factor data (Table 4). The 3 genetic risk factors (CKS1Bamplification, chromosome band 1304 deletion, and metaphase karyotypeabnormalities) all independently conferred both inferior event-free andoverall survival, whereas hypo-albuminemia was the only one of threestandard prognostic factors that retained adverse implications for bothendpoints examined. Collectively, these 6 variables accounted for 46%and 33% of variability in survival and event-free survival,respectively, with the 3 standard, non-genetic parameters contributingonly an additional 7.2% and 7.4%. CKS1B amplification was an independentpredictor of outcome both as a 0-100 scale index and as a two-groupcategory (Table 4A and B) after adjustment for the variables mentionedabove and for the plasma cell labeling index.

Paired CKS1B expression data at diagnosis and relapse, available in 32cases, revealed increased expression in 84% at relapse (P=0.0001, FIG.7), which was especially prominent in patients with quartile 1-3expression levels at diagnosis. Paired CKS1B copy number data atdiagnosis and relapse were available in 17 patients: of 7 lackingamplification at diagnosis, 4 demonstrated greater than equal to 3copies at relapse; of 10 cases with 3 copies at diagnosis, 4 hadacquired greater than equal to 4 copies at relapse; but 2 cases with 4or more copies at diagnosis exhibited no further amplification atrelapse.

Additionally, the relationship between CKS1B expression, CKS1Bamplification and genetic subgroups was examined. The frequency of CKS1Bquartile 4 expression varied among previously reported genetic subgroups(Fonseca et al., 2004) (Table 7A). With respect to gene expression-basedtranslocations, nearly two-thirds of patients with MAF or MAFBactivation, one-third each with FGFR3/MMSET and CCND1 activation, andonly 18% without these translocations had CKS1B hyper-activation(P<0.0001). When examined in the context of metaphase karyotypes, CKS1Bquartile 4 expression was present in approximately 20% of cases withhyperdiploid or normal, i.e. uninformative, karyotypes, whereas thisfeature was seen in nearly 50% of patients with hypodiploid and othercytogenetic abnormalities (P=0.0002).

In a separate multivariate analysis that was adjusted for geneticsubgroups, CKS1B quartile 4 expression remained an independent adverseoutcome predictor (Table 7B); the gene expression-derived translocationcategory as a whole conferred inferior event-free (P=0.034) but notoverall survival (P=0.261); which was consistent with published data(Fonseca et al., 2004), CCND1 activation impacted both endpointsfavorably. While not adjusted for the multiple log rank tests thatidentified the 70 genes, this analysis suggested that CKS1B expressionretained explanatory power within relevant genetic subgroups.

TABLE 7A Relationship between genetic abnormalities and CKS1B expressionin quartile 4 CKS1B Abnormality n/347 Q4 Category^(†) (%) n (%) P-Value*Expression-derived translocation t(11; 14) 60 (17.3) 20 (33.3) <0.0001t(4; 14) 48 (13.8) 17 (35.4) t(14; 16) & t(14; 20) 14 (4.0) 9 (64.3) NoTranslocation Spike 225 (64.8) 41 (18.2) Metaphase karyotypeHyperdiploid 55 (15.9) 10 (18.2) 0.0002 Non-hyperdiploid 48 (13.8) 24(50.0) Other Cytogenetics 9 (2.6) 4 (44.4) Abnormality No Cytogenetics235 (67.7) 49 (20.9) Abnormality Chromosome 13 Deletion n/334 No 224(67.1) 47 21.0 0.02 Yes 110 (32.9) 37 33.6 ^(†)Translocations weredetermined from the expression spikes t(11; 14) = CCND1, t(4: 14) =FGFR3/MMSET, t(14; 16) = MAF and t(14; 20) = MAFB. Aneuploidy and othercytogenetic abnormalities were determined from cytogenetics, for which 4observations were missing. *Fisher's exact test of the independence ofeach category and CKS1B 4th quartile membership. Under the nullhypothesis, Q4 contains on average 25% of patients within each level,corresponding to a proportional distribution across Q1-3 and Q4.

TABLE 7B Multivariate analysis of CKS1B quartile 4 expression andcytogenetic abnormalities^(†) Event-Free Survival Survival HR P^(‡) HRP^(‡) CKS1B Q4 1.97 0.003 2.16 0.005 Expression-derived translocation*t(11; 14) 0.59 0.034 0.82 0.261 t(4; 14) 1.67 1.77 t(14; 16) & t(14; 20)1.48 1.12 Metaphase karyotype** Hyperdiploid 1.75 0.006 1.84 0.013Non-hyperdiploid 2.29 2.56 Other Cytogenetics 2.35 2.71 Abnormality r²0.218 0.223 Events/Deaths 97 63 ^(†)N = 347. Of 351 patients withexpression data, 4 are missing cytogenetics. ^(‡)Partial likelihoodratio test for the overall effect of the category. *The P-value formodification of the CKS1B effect on EFS by translocation subgroup is0.74. **The P-value for modification of the CKS1B effect on EFS bykaryotype subgroup is 0.27 and for survival it is 0.17. For survival,the hazard ratio for CKS1B is estimated to be 4.2 times higher in thenon-hyperdiploid group compared to those with no abnormalities, withhazard ratios roughly the same for the other groups.Furthermore, western blot analysis of nuclear protein from plasma cellsfrom 27 newly diagnosed myeloma cases and 7 myeloma cell lines showed astrong correlation between CKS1B mRNA and protein, but no correlationbetween CDKN1B gene expression and CKS1B gene expression, protein levelsor CDKN1B protein levels. However, CKS1B protein and CDKN1B proteinlevels showed an inverse correlation (FIG. 8). The cause for rarediscrepancies (e.g. high CKS1B protein in the absence of elevated geneexpression, was not clearly understood. Uniform histone 1A proteinlevels indicated equal protein loading across all samples. Cytoplasmicand non-phosphorylated-thr-187-CDKN1B levels were not altered in myelomacell lysates with respect to CKS1B expression. Levels of CDKN1B proteinwere not correlated with the mRNA levels of SKP2.Discussion:

Global gene expression analyses of highly purified plasma cells fromnewly diagnosed myeloma patients identified 70 genes that weresignificantly correlated with early disease-related mortality (medianfollow-up of 22 months). Importantly, 30% of these genes mapped tochromosome 1 suggesting an important role for this chromosome in myelomadisease progression. The increased expression of 1q genes and reducedexpression of 1p genes were consistent with cytogenetic data of frequent1q gains and 1p losses in myeloma karyotypes. (Nilsson et al., 2003;Gutierrez et al., 2004). Additionally, tandem duplications and jumpingtranslocations involving 1q21, caused by decondensation ofpericentromeric heterochromatin, are features of end stage disease(Sawyer et al., 2005; Sawyer et al., 1998; Le Baccon et al., 2001).

Over-expression/amplification of CKS1B, mapping to 1q21, was linked topoor prognosis in early follow-up of newly diagnosed myeloma. The roleof CKS1B in controlling SCFSkp2-mediated ubiquitinylation andproteasomal degradation of the cyclin-dependent kinase inhibitor CDKN1Bmade it an attractive candidate gene. CKS1B protein levels werecorrelated with gene expression and were both inversely correlated withCDKN1B protein levels. Investigations in S. cerevisiae have demonstratedan essential role of cks1 in promoting mitosis by modulating thetranscriptional activation of CDC20 (Morris et al., 2003). CKS1B andCDC20 expression were strongly correlated (r=0.78; p<0.0001, data notshown), consistent with CKS1B promoting mitosis by regulating CDC20expression in human cells. Thus, a gene dosage-related increase in CKS1Bexpression might lead to enhanced degradation of CDKN1B and alsoactivation of CDC20 in myeloma.

In the context of recently recognized prognostically relevant geneticsubgroups, CKS1B hyper-activation was less frequent in cases withhyperdiploid and normal karyotypes; one-third of those withCCND1-translocations had high CKS1B levels; and up to two-thirds ofhigh-risk entities, MAF, MAFB and hypodiploidy displayed CKS1Bhyper-activation (Table 7A). In addition to conferring a poor prognosisamong newly diagnosed patients, CKS1B over-expression and amplificationwere common at relapse in patients lacking these features at diagnosis.Thus, it will be important to determine whether CKS1B amplificationemerges in all subgroups and, when present, portends rapid diseaseprogression and death. Moreover, since 1q21 amplification is frequentobservation in many advanced solid and hematological malignancies, itwill be important to determine if CKS1B gene amplification is associatedwith disease aggressiveness in a larger proportion of cancers.

Furthermore, CKS1B gene amplification along with chromosome 13q14deletion and abnormal metaphase cytogenetics accounted for almost 40% ofthe observed survival variability, underscoring that myeloma risk isbest assessed by molecular and cellular genetic tests. Routineapplication of such studies, performed on a single bone marrow sample,is therefore recommended for appropriate patient stratification intherapeutic trial design. Additionally, the survival impact of newagents, such as bortezomib and thalidomide and its derivatives, will beprofound if their clinical efficacy also extends to genetically definedhigh-risk myeloma, which has not been investigated. Since CKS1B appearsto directly or indirectly interact with ubiquitin ligases and/or theproteasome to regulate multiple cell cycle checkpoints (Pagano andBenmaamar, 2003), new therapeutic strategies that directly target CKS1Bor related pathways may represent novel, and more specific, means oftreating de novo high-risk myeloma and may prevent its secondaryevolution.

Given the negative impact of chromosome band 13q14 deletion on survival,it is noteworthy that reduced expression of a single gene mapping tochromosome 13q14, RFP2/LEU5, which was previously identified as acandidate tumor suppressor gene with significant homology to BRCA1(Kapandaze et al., 1998), was significantly linked to poor survival inthis analysis, and suggests that an in-depth investigation of RFP2function and mutation analysis in myeloma is warranted.

Additionally, cyclin D dysregulation is a common event in cancer andcontributes to tumorigenesis by promoting hyperphosphorylation of theRB1 protein and activation of E2F target genes important in promoteingtransition through early G1 to S checkpoint of the cell cycle. Previousstudy had reported that dysregulated expression of one of the threeD-type cyclins was likely to be a unifying initiating genetic lesion inmultiple myeloma. Based on the available information and the resultspresented herein, a multistep pathogenic model of myelomagensis iscontemplated in which activation of a D type cyclin is an earlyinitiating event and CKS1B amplification is a progression event,resulting in loss of both early and late G1 to S checkpoints of the cellcycle and establishment of an aggressive, multidrug resistant disease.The following references are cited herein:

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Any patents or publications mentioned in this specification areindicative of the levels of those skilled in the art to which theinvention pertains. Further, these patents and publications areincorporated by reference herein to the same extent as if eachindividual publication was specifically and individually indicated to beincorporated by reference.

What is claimed is:
 1. A detection method comprising: obtaining anisolated nucleic acid sample from plasma cells isolated from a multiplemyeloma patient; and measuring gene expression levels of GNG10, PNPLA4,KIAA1754, AHCYL1, MCLC, EVI5, AD-020, PARG1, CTBS, FUCA1, RFP2,FLJ20489, LTBP1, TRIP13, AIM2, SELI, SLC19A1, LARS2, OPN3, ASPM, CCT2,UBE21, SIK6, FLJ13052, FLJ12525, BIRC5, CKS1B, CKAP1, MGC57827,DKFZp7790175, PFN1, ILF3, IF116, TBRG4, PAPD1, EIF2C2, MGC4308, ENO1,DSG2, EXOSC4, 7AGLN2, RUVBL1, ALDOA, CPSF3, MGC15606, LGALS1, RADI8,SNX5, PSMD4, RAN, KIF14, CBX3, TMPO, DKFZP586L0724, WEE1, ROBO1, TCOF1,YWHAZ, and MPHOSPH1 in the plasma cells by contacting the isolatednucleic acid sample with nucleic acid probes that hybridize to each geneand detecting the complex formed between the plasma cell RNA and eachprobe, wherein the method comprises detecting reduced expression ofGNG10, PNPLA4, KIAA1754, AHCYL1, MCLC, EVI5, AD-020, PARG1, CTBS, FUCA1,RFP2, FLJ20489, or LTBP1, relative to a control from a patient having afavorable prognosis, or detecting increased expression of TRIP13, AIM2,SELI, SLC19A1, LARS2, OPN3, ASPM, CCT2, UBE21, STK6, FLJ13052, FLJ12525,BIRC5, CKS1B, CKAP1, MGC57827, DKFZp7790175, PFN1, ILF3, IFI16, TBRG4,PAPD1, EIF2C2, MGC4308, EN1L, DSG2, EXOSC4, TAGLN2, RUVBL1, ALDOA,CPSF3, MGC15606, LGALS1, RAD18, SNX5, PSMD4, RAN, KIF14, CBX3, TMPO,DKFZP586L0724, WEE1, ROBO1, TCOF1, YWHAZ, or MPHOSPH1, relative to acontrol from a patient having a favorable prognosis.
 2. The method ofclaim 1, wherein measuring the gene expression levels comprisesgenerating cDNA from the isolated nucleic acid sample isolated from theplasma cells.
 3. The method of claim 1, wherein the patient isundergoing, or previously underwent, treatment comprising high-dosechemotherapy.
 4. The method of claim 3, wherein the high dosechemotherapy comprises bortezomib, thalidomide, or a combinationthereof.
 5. The method of claim 1, wherein the patient is undergoing, orpreviously underwent, treatment comprising autologous peripheral bloodstem cell transplantation.
 6. The method of claim 1, wherein the nucleicacid sample is artificially and detectably labeled.
 7. The method ofclaim 6, wherein the gene expression levels are measured by detecting acomplex between the artificially and detectably labeled nucleic acidsample and a synthetic microarray.
 8. The method of claim 1, wherein theplasma cells are CD138+ plasma cells.